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Add CRAM and BAM support to last/mafconvert #7391

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merged 9 commits into from
Feb 1, 2025
Merged

Add CRAM and BAM support to last/mafconvert #7391

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5bd09a4
Add samtools to the image of last/maconvert, for CRAM/BAM support.
charles-plessy Jan 29, 2025
6d52598
Correct wrong description in last/mafconvert tests.
charles-plessy Jan 29, 2025
2e1c112
Add BAM support.
charles-plessy Jan 29, 2025
e47ceba
Add CRAM support to last/mafconvert
charles-plessy Jan 29, 2025
78254a8
Add samtools to the conda environment
charles-plessy Jan 30, 2025
43ba1ee
Request the input genome to be indexed.
charles-plessy Jan 30, 2025
c7ad3af
Change input of last/mafconvert to match the output of samtools/faidx
charles-plessy Jan 31, 2025
b3e4c46
Adapt to previous change of input channels.
charles-plessy Jan 31, 2025
d26919e
Merge branch 'master' into maf-convert-cram-bam
charles-plessy Feb 1, 2025
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44 changes: 31 additions & 13 deletions modules/nf-core/last/mafconvert/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,24 +4,29 @@ process LAST_MAFCONVERT {

conda "${moduleDir}/environment.yml"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/db/db0b5de918238f07ec1ca668be942397da85e26aa582f8927ac37c70896303cf/data'
: 'community.wave.seqera.io/library/last:1608--f41c047f7dc37e30'}"
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/37/379183a78f725c3a8f2c4dda2f73ad452e57cc895239938fc97281d7bd74ffbf/data'
: 'community.wave.seqera.io/library/last_samtools:e2b51d2d9a1ce9fa'}"

input:
tuple val(meta), path(maf)
val(format)
path(fasta)

output:
tuple val(meta), path("*.axt.gz"), optional:true, emit: axt_gz
tuple val(meta), path("*.blast.gz"), optional:true, emit: blast_gz
tuple val(meta), path("*.blasttab.gz"), optional:true, emit: blasttab_gz
tuple val(meta), path("*.chain.gz"), optional:true, emit: chain_gz
tuple val(meta), path("*.gff.gz"), optional:true, emit: gff_gz
tuple val(meta), path("*.html.gz"), optional:true, emit: html_gz
tuple val(meta), path("*.psl.gz"), optional:true, emit: psl_gz
tuple val(meta), path("*.sam.gz"), optional:true, emit: sam_gz
tuple val(meta), path("*.tab.gz"), optional:true, emit: tab_gz
path "versions.yml" , emit: versions
tuple val(meta), path("*.axt.gz"), optional:true, emit: axt_gz
tuple val(meta), path("*.bam"), optional:true, emit: bam
tuple val(meta), path("*.blast.gz"), optional:true, emit: blast_gz
tuple val(meta), path("*.blasttab.gz"), optional:true, emit: blasttab_gz
tuple val(meta), path("*.chain.gz"), optional:true, emit: chain_gz
tuple val(meta), path("*.cram"), path(fasta), optional:true, emit: cram
path("*.fai"), optional:true, emit: fai
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Suggested change
tuple val(meta), path("*.cram"), path(fasta), optional:true, emit: cram
path("*.fai"), optional:true, emit: fai
tuple val(meta), path("*.cram"), optional:true, emit: cram

fasta is an input file so shouldn't be in the output section,
fai should also be an input file :)

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At the moment I need path(fasta) in the cram output channel because I did not find another way to access that file during the tests. Can you help me to solve that problem?

tuple val(meta), path("*.gff.gz"), optional:true, emit: gff_gz
path("*.gzi"), optional:true, emit: gzi
tuple val(meta), path("*.html.gz"), optional:true, emit: html_gz
tuple val(meta), path("*.psl.gz"), optional:true, emit: psl_gz
tuple val(meta), path("*.sam.gz"), optional:true, emit: sam_gz
tuple val(meta), path("*.tab.gz"), optional:true, emit: tab_gz
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -31,7 +36,20 @@ process LAST_MAFCONVERT {
def prefix = task.ext.prefix ?: "${meta.id}"
"""
set -o pipefail
maf-convert $args $format $maf | gzip --no-name > ${prefix}.${format}.gz

case $format in
bam)
maf-convert $args -d sam $maf | samtools view -b -o ${prefix}.${format}
;;
cram)
# CRAM output is not supported if the genome is compressed with something else than bgzip
samtools faidx $fasta
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maf-convert $args -d sam $maf | samtools view -Ct $fasta -o ${prefix}.${format}
;;
*)
maf-convert $args $format $maf | gzip --no-name > ${prefix}.${format}.gz
;;
esac

# maf-convert has no --version option but lastdb (part of the same package) has.
cat <<-END_VERSIONS > versions.yml
Expand Down
39 changes: 39 additions & 0 deletions modules/nf-core/last/mafconvert/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,11 @@ input:
type: string
description: Output format (one of axt, blast, blasttab, chain, gff, html, psl,
sam, or tab)
- - fasta:
type: file
description: Genome file in FASTA format for CRAM conversion. If compressed it
must be done in BGZF format (like with the bgzip tool).
pattern: "*.{fasta,fasta.gz,fasta.bgz,fasta.bgzf}"
output:
- axt_gz:
- meta:
Expand All @@ -40,6 +45,16 @@ output:
type: file
description: Gzipped pairwise alignment in Axt (Blastz) format (optional)
pattern: "*.axt.gz"
- bam:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1', single_end:false ]`
- "*.bam":
type: file
description: Pairwise alignment in BAM format (optional)
pattern: "*.bam"
- blast_gz:
- meta:
type: map
Expand Down Expand Up @@ -70,6 +85,25 @@ output:
type: file
description: Gzipped pairwise alignment in UCSC chain format (optional)
pattern: "*.chain.gz"
- cram:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'sample1', single_end:false ]`
- "*.cram":
type: file
description: Pairwise alignment in CRAM format (optional)
pattern: "*.cram"
- fasta:
type: file
description: Genome file to recover sequences from the CRAM file (optional)
pattern: "*.{fasta,fasta.gz,fasta.bgz,fasta.bgzf}"
- fai:
- "*.fai":
type: file
description: Genome file index generated during CRAM conversion (optional)
pattern: "*.fai"
- gff_gz:
- meta:
type: map
Expand All @@ -80,6 +114,11 @@ output:
type: file
description: Gzipped pairwise alignment in GFF format (optional)
pattern: "*.gff.gz"
- gzi:
- "*.gzi":
type: file
description: Genome file index generated during CRAM conversion (optional)
pattern: "*.gzi"
- html_gz:
- meta:
type: map
Expand Down
62 changes: 60 additions & 2 deletions modules/nf-core/last/mafconvert/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ nextflow_process {
tag "last"
tag "last/mafconvert"

test("sarscov2 - bam") {
test("sarscov2 - psl") {

when {
process {
Expand All @@ -19,6 +19,7 @@ nextflow_process {
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true)
]
input[1] = 'psl'
input[2] = []
"""
}
}
Expand All @@ -32,7 +33,63 @@ nextflow_process {

}

test("sarscov2 - bam - stub") {
test("sarscov2 - bam") {

when {
process {
"""
input[0] = [
[ id:'contigs.genome' ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true)
]
input[1] = 'bam'
input[2] = []
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.bam.collect { bam(it[1]).getSamLines() },
process.out.versions
).match() }
)
}

}

test("sarscov2 - cram") {

when {
process {
"""
input[0] = [
[ id:'contigs.genome' ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true)
]
input[1] = 'cram'
input[2] = [
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.cram.collect { cram(it[1], it[2]).getSamLines() },
process.out.versions
).match() }
)
}

}

test("sarscov2 - psl - stub") {

options "-stub"
when {
Expand All @@ -43,6 +100,7 @@ nextflow_process {
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true)
]
input[1] = 'psl'
input[2] = []
"""
}
}
Expand Down
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